Publications

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  1. Ehteda A, Simon S, Franshaw L, Giorgi FM, Liu J, Joshi S, Rouaen JRC, Pang CNI, Pandher R, Mayoh C, Tang Y, Khan A, Ung C, Tolhurst O, Kankean A, Hayden E, Lehmann R, Shen S, Gopalakrishnan A, Trebilcock P, Gurova K, Gudkov AV, Norris MD, Haber M, Vittorio O, Tsoli M, Ziegler D. Dual targeting of the epigenome via FACT complex and histone deacetylase is a potent treatment strategy for DIPG. Cell Reports 2021.
  2. Gamble LD, Purgato S, Henderson MJ, Di Giacomo S, Russell AJ, Pigini P, Murray J, Valli E, Milazzo G, Giorgi FM, Cowley M, Ashton LJ, Bhalshankar J, Schleiermacher G, Rihani A, Van Maerken T, Vandesompele J, Speleman  F, Versteeg R, Koster J, Eggert A, Noguera R, Stallings RL, Tonini GP, Fong K, Vaksman Z, Diskin SJ, Maris JM, London WB, Marshall GM, Ziegler DS, Hogarty MD, Perini G, Norris MD, Haber M. A g316a polymorphism in the ornithine decarboxylase gene promoter modulates mycn‐driven childhood neuroblastoma. Cancers 2021.
  3. Ortuso F, Mercatelli D, Huzzi PH, Giorgi FM. Structural Genetics of circulating variants affecting the SARS-CoV-2 Spike / human ACE2 complex. Journal of Biomolecular Structure and Dynamics 2021.
  4. Mercatelli D, Balboni N, Palma A, Aleo E, Sanna PP, Perini G, Giorgi FM. Single-cell gene network analysis and transcriptional landscape of MYCN-amplified neuroblastoma cell lines. Biomolecules 2021.
  5. Paull EO, Aytes A, Jones SJ, Subramaniam PS, Giorgi FM, Douglass EF, Tagore S, Chu B, Vasciaveo A, Zheng S, Verhaak R, Abate-Shen C, Alvarez MJ, Califano A. A modular master regulator landscape controls cancer transcriptional identity.  Cell 2021.
  6. Broyde J, Simpson DR, Murray D, Paull EO, Chu BW, Tagore S, Jones SJ, Griffin AT, Giorgi FM, Lachmann A, Jackson P, Sweet-Cordero EA, Honig B, Califano A. Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses.  Nature Biotechnology 2021.
  7. Mercatelli D, Triboli L, Fornasari E, Ray F, Giorgi FM. Coronapp: A web application to annotate and monitor SARS-CoV-2 mutations. Journal of Medical Virology 2021.
  8. Mercatelli D, Holding AN, Giorgi FM. Web tools to fight pandemics: the COVID-19 experience. Briefings in Bioinformatics 2021.
  9. Gardini E, Giorgi FM, Decherchi S, Cavalli A. Spathial: an R package for the evolutionary analysis of biological data. Bioinformatics, 2020.
  10. Lopez G, Egolf LE, Giorgi FM, Diskin SJ, Margolin AA. Svpluscnv: analysis and visualization of complex structural variation data. Bioinformatics 2020.
  11. Galicia JC, Guzzi PH, Giorgi FM, Khan AA. Predicting the response of the dental pulp to SARS-CoV2 infection: a transcriptome-wide effect cross-analysis. Genes & Immunity 2020.
  12. Bui LT, Shukla V, Giorgi FM, Trivellini A, Perata P, Licausi F, Giuntoli B. Differential submergence tolerance between juvenile and adult Arabidopsis plants involves the ANAC017 transcription factor. Plant Journal 2020.
  13. Voli F, Valli E, Lerra L, Kimpton K, Saletta F, Giorgi FM, Mercatelli D, Rouaen JRC, Shen S, Murray JE, Ahmed-Cox A, Cirillo G, Mayoh C, Beavis PA, Haber M, Trapani JA, Kavallaris M, Vittorio O. Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion. Cancer Research 2020.
  14. Mercatelli D, Bortolotti M, Giorgi FM. Transcriptional network inference and master regulator analysis of the response to ribosome-inactivating proteins in leukemia cells. Toxicology 2020.
  15. Mercatelli D, Giorgi FM. Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Frontiers in Microbiology 2020.
  16. Milazzo G, Mercatelli D, Di Muzio G, Triboli L, De Rosa P, Perini G, Giorgi FM. Histone Deacetylases (HDACs): Evolution, Specificity, Role in Transcriptional Complexes, and Pharmacological Actionability. Genes, 2020
  17. Guzzi PH, Mercatelli D, Ceraolo C, Giorgi FM. Master Regulator Analysis of the SARS-CoV-2/Human interactome. Journal of Clinical Medicine 2020.
  18. Mercatelli D, Lopez-Garcia G, Giorgi FM. corto: a lightweight R package for Gene Network Inference and Master Regulator Analysis. Bioinformatics 2020.
  19. Giorgi FM. Gene network reverse engineering: The Next Generation. Biochimica et Biophysica Acta GRM, 2020.
  20. Ceraolo C, Giorgi FM. Genomic variance of the 2019-nCoV coronavirus. Journal of Medical Virology, 2020.
  21. Mercatelli D, Scalambra L, Triboli L, Ray F, Giorgi FM. Gene regulatory network inference resources: A practical overview. Biochimica et Biophysica Acta GRM 2020.
  22. Paz-Elizur T, Leitner-Dagan Y, Meyer KB, Markus B, Giorgi FM, O’Reilly M, Kim H, Evgy Y, Fluss R, Freedman LS, Rintoul RC, Ponder B, Livneh Z. DNA-Repair Biomarker for Lung Cancer Risk and its Correlation with Airway Cells Gene Expression. JNCI Cancer Spectrum 2020.
  23. Mercatelli D, Ray F, Giorgi FM. Pan-Cancer and Single-Cell modelling of genomic alterations through gene expression. Frontiers in Genetics 2019.
  24. Giorgi FM, Holding AN, Donnelly A, Cullen AE, Nagarajan S, Seth LA, Markowetz F. VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer. Genome Biology 2019.
  25. Gamble LD, Purgato S, Murray J, Xiao L, Yu DMT, Hanssen KM, Giorgi FM, Carter DR, Gifford AJ, Valli E, Milazzo G, Kamili A, Mayoh C, Liu B, Eden G, Sarraf S, Allan S, Di Giacomo S, Flemming CL, Russell AJ, Cheung BB, Oberthuer A, London WB, Fischer M, Trahair TN, Fletcher JI, Marshall GM, Ziegler DS, Hogarty MD, Burns MR, Perini G, Norris MD, Haber M. Inhibition of polyamine synthesis and uptake reduces tumor progression and prolongs survival in mouse models of neuroblastoma. Science Translational Medicine 2019.
  26. Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ. A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell 2018.
  27. Giuntoli B, Shukla V, Maggiorelli F, Giorgi FM, Lombardi L, Perata P, Licausi F. Age-dependent regulation of ERF-VII transcription factor activity in Arabidopsis thaliana. Plant & Cell Environment 2017
  28. Sibout S, Proost S, Hansen BO, Vaid N, Giorgi FM, …, Persson S, Mutwil M. Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon. New Phytologist 2017.
  29. Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, Ding BB, Ye BH, Califano A. Dissecting the mutational landscape of cancer by integrative inference and analysis of protein activity. Nature Genetics 2016.
  30. Giorgi FM, Lachmann A, Garcia GL, Califano A. ARACNe-AP: Gene Network Reverse Engineering through Adaptive Partitioning inference of Mutual Information. Bioinformatics 2016.
  31. Giorgi FM, Lachmann A, Alvarez MJ, Califano A. Detection and removal of spatial bias in multi-well assays. Bioinformatics 2016.
  32. Sepulveda JL, Gutierrez-Pajares JL, Luna A, Yao Y, Tobias JW, Thomas S, Woo Y, Giorgi FM, Komissarova EV, Califano A, Wang TC, Sepulveda AR. High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing. Modern Pathology 2016.
  33. Hughes JM, Salvatori B, Giorgi FM, Bozzoni I, Fatica A. CEBPA-regulated lncRNAs, new players in the study of acute myeloid leukemia. J Hematol Oncol 2014.
  34. Giorgi FM, Lopez G, Woo JH, Califano, A Bansal M. Inferring protein modulation from gene expression data using Conditional Mutual Information. PLOS One 2014.
  35. Tosetti R, Tardelli F, Tardiello F, Zaffalon V, Giorgi FM, Guidi L, Trainotti L, Bonghi C and Tonutti P. Molecular and biochemical responses to wounding in mesocarp of peach (Prunus persica L. Batsch) ripe fruits. Postharvest Biology and Technology 2014.
  36. Del Fabbro C, Scalabrin S, Morgante M and Giorgi FM. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLOS ONE, 2013.
  37. Lee YP, Giorgi FM, Lohse M, Usadel B, Klages S, Reinhardt R, Hincha DK. Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea. BMC Genomics 2013.
  38. Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV. The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. Briefings in Bioinformatics 2013.
  39. Giorgi FM, Del Fabbro C, Licausi F. Comparative study of RNA-seq- and Microarray- derived coexpression networks in Arabidopsis thaliana. Bioinformatics 2013.
  40. Santaniello A, Giorgi FM, Di Tommaso D, Di Tommaso G, Piaggesi A, Perata  P. Genomic approaches to unveil the physiological pathways activated in Arabidopsis treated with plant-derived raw extracts. Acta Horticulturae 2012.
  41. Paparelli E, Gonzali S, Parlanti S, Novi G, Giorgi FM, Licausi F, Kosmacz M, Feil R, Lunn J, Brust H, van Dongen J, Steup M, Perata P. Misexpression of a chloroplast aspartyl protease leads to severe growth defects and alters carbohydrate metabolism in Arabidopsis. Plant Physiology 2012.
  42. Giorgi FM, Vasilevski A, Bertinetti L, Usadel B. LASSO modeling of the Arabidopsis thaliana seed/seedling Transcriptome: a model case for detection of novel mucilage and pectin metabolism genes. Molecular Biosystems 2012.
  43. Licausi F, Kosmacz M, Weits DA, Giuntoli B, Giorgi FM, Voesenek LACJ, Perata P, Van Dongen JT. Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization. Nature 2011.
  44. Ryngajllo M, Childs L, Lohse M, Giorgi FM, Lude A, Selbig J and Usadel B. SLocX: predicting subcellular localization of Arabidopsis proteins leveraging gene expression data. Frontiers in Plant Science 2011.
  45. Giorgi FM, Licausi F, Schmaelzlin E, Usadel B, Perata P, van Dongen J and Geigenberger P. HRE-Type genes are regulated by growth-related changes in Internal oxygen concentrations during the normal development of potato (Solanum tuberosum) tubers, Plant & Cell Physiology 2011.
  46. Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z and Persson S. PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species, Plant Cell 2011.
  47. Licausi F, Giorgi FM, Zenoni S, Osti F, Pezzotti M and Perata P. Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera, BMC Genomics 2010.
  48. Giorgi FM, Bolger AM, Lohse M and Usadel B. Algorithm-driven Artifacts in median polish summarization of Microarray data, BMC Bioinformatics 2010.
  49. Civril F, Wehenkel A, Giorgi FM, Santaguida S, Di Fonzo A, Grigorean G, Ciccarelli FD, Musacchio A. Structural analysis of the RZZ complex reveals common ancestry with multisubunit vesicle tethering machinery, Structure 2010.
  50. Lohse M, Nunes-Nesi A, Krüger P, Nagel A, Hannemann J, Giorgi FM, Childs L, Osorio S, Walther D, Selbig J, Sreenivasulu N, Stitt M, Fernie AR, Usadel B. Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis, Plant Physiology 2010.
  51. Mutwil M, Ruprecht C, Giorgi FM, Bringmann M, Usadel B, Persson S. Transcriptional wiring of cell wall-related genes in Arabidopsis, Molecular Plant 2009.
  52. Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ. Co-expression tools for plant biology: opportunities for hypothesis generation and caveats, Plant & Cell Environment 2009.
  53. Rambaldi D, Giorgi FM, Capuani F, Ciliberto A, Ciccarelli FD. Low duplicability and network fragility of cancer genes, Trends in Genetics 2008.